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gbouras13 / pharokka

fast phage annotation program
MIT License
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Quick question #285

Closed r4carson closed 1 year ago

r4carson commented 1 year ago

Description

I was just wondering if the meta -m flag assemble a phage genome or should I assemble the genome first? Does meta -m flag only combine contigs from the consensus sequence?

gbouras13 commented 1 year ago

Hi @r4carson,

Thanks for the great question!

Pharokka does not do assembly at all, nor does it combine contigs. All -m does is tell pharokka to expect multiple contigs in the input file, so it can do some things in the background to make it run a lot faster. If you have multiple contigs from a metagenome, definitely use -m, otherwise don’t.

For assembly I’d recommend metaspades, megahit or flye depending on your reads. For the combining of assemblies I’d recommend phables https://github.com/Vini2/phables.

George

gbouras13 commented 1 year ago

I'm closing this now @r4carson - any other questions feel free to ask them.